http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&feed=atom&action=history
Minnesota/25 June 2009 - Revision history
2024-03-29T15:12:25Z
Revision history for this page on the wiki
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http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=34807&oldid=prev
Patsmad at 22:04, 30 July 2009
2009-07-30T22:04:28Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Patrick'''<br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">I got back the analysis of the models submitted yesterday. I submitted a base model shown here:<br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><center><gallery widths=400 heights=300></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badBase.jpg|Figure 1 - Base TTN Model</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></gallery></center><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">I also changed the tendency for tetO1 to detach from the tetR2:tetO1:2aTc complex (k=100000 1/s initially) by lower or higher an order of magnitude:<br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><center><gallery widths=300 heights=200></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk2u.jpg|Figure 2 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk2d.jpg|Figure 3 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></gallery></center><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><center><gallery widths=300 heights=200></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk2u.jpg|Figure 4 - Increased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk2d.jpg|Figure 5 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></gallery></center><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><center><gallery widths=300 heights=200></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk12u.jpg|Figure 6 - Increased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Image:badk12d.jpg|Figure 7 - Decreased Rate of tetO1 Detachment from tetR2:tetO1:2aTc/aTc complex</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></gallery></center><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">None of the graphs were particularly interesting. I also submitted two more jobs: '''smad_tetRu/d''' which either increased or decreased the rate of synthesis of tetR2 (reaction 44, k = 1E-11 M/s initially) by an order of magnitude.<br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">'''Ben'''<br></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model.</div></td></tr>
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Patsmad
http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=34740&oldid=prev
Bswiniar at 21:03, 30 July 2009
2009-07-30T21:03:44Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">This model does indeed show some different leakiness, which is definitely a good thing, although the leakiness is still too high for an accurate model. Still, the problem remains where the model peaks and decreases instead of reaching a steady state.</ins></div></td></tr>
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Bswiniar
http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=34738&oldid=prev
Bswiniar at 21:02, 30 July 2009
2009-07-30T21:02:04Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Reverse Kinetic Constant</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Reverse Kinetic Constant</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2||<del class="diffchange diffchange-inline">311000</del>||</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2||<ins class="diffchange diffchange-inline">1200000</ins>||</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2||<del class="diffchange diffchange-inline">311000</del>||</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2||<ins class="diffchange diffchange-inline">1200000</ins>||</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>||RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2||<del class="diffchange diffchange-inline">311000</del>||</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>||RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2||<ins class="diffchange diffchange-inline">1200000</ins>||</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td></tr>
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Bswiniar
http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=34737&oldid=prev
Bswiniar at 21:01, 30 July 2009
2009-07-30T21:01:44Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''[[Minnesota/24 June 2009|Go to Previous Day (June 24)]]'''|| width=158|'''[[Minnesota/26 June 2009|Go to Next Day (June 26)]]'''</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|}</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><br></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">{| class="wikitable" style="text-align:center" border = "1"</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Reaction</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Forward Kinetic Constant</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">! Reverse Kinetic Constant</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2||311000||</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2||311000||</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">||RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2||311000||</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></div></td></tr>
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Bswiniar
http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=32953&oldid=prev
Bswiniar at 19:31, 29 July 2009
2009-07-29T19:31:34Z
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:Tnnatcvariesleaky5.jpg|480px]][[Image:Tnnexperiment.jpg|480px]]<br></ins></div></td></tr>
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Bswiniar
http://2009.igem.org/wiki/index.php?title=Minnesota/25_June_2009&diff=30219&oldid=prev
Bswiniar: New page: {|style="align:left" width="965" |- |''' Back to Notebook Home''' |- |'''Go to Previous Day (June 24)'''|| width=158|'''[[Minnesota/...
2009-07-28T15:38:15Z
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